In the absence of clear molecular insight, the biological mechanism behind the use of growth factors applied in osteochondral regeneration is still unresolved. The present study aimed to resolve whether multiple growth factors applied to muscle tissue , such as TGF-β3, BMP-2 and Noggin, can lead to appropriate tissue morphogenesis with a specific osteochondrogenic nature, thereby revealing the underlying molecular interaction mechanisms during the differentiation process. Interestingly, although the results showed the typical modulatory effect of BMP-2 and TGF-β3 on the osteochondral process, and Noggin seemingly downregulated specific signals such as BMP-2 activity, we also discovered a synergistic effect between TGF-β3 and Noggin that positively influenced tissue morphogenesis. Noggin was observed to upregulate BMP-2 and OCN at specific time windows of culture in the presence of TGF-β3, suggesting a temporal time switch causing functional changes in the signaling protein. This implies that signals change their functions throughout the process of new tissue formation, which may depend on the presence or absence of specific singular or multiple signaling cues. If this is the case, the signaling cascade is far more intricate and complex than originally believed, warranting intensive future investigations so that regenerative therapies of a critical clinical nature can function properly.